
PathActMarker: an R package for inferring pathway activity of complex diseases
Xingyi LI, Jun HAO, Zhelin ZHAO, Junming LI, Xingyu LIAO, Min LI, Xuequn SHANG
Front. Comput. Sci. ›› 2025, Vol. 19 ›› Issue (3) : 193908.
PathActMarker: an R package for inferring pathway activity of complex diseases
[1] |
Drier Y, Sheffer M, Domany E . Pathway-based personalized analysis of cancer. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110( 16): 6388–6393
|
[2] |
Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov J P . Molecular signatures database (MSigDB) 3.0. Bioinformatics, 2011, 27( 12): 1739–1740
|
[3] |
Kanehisa M, Goto S. Kegg: kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 2000, 28(1): 27–30
|
[4] |
Li X, Li M, Xiang J, Zhao Z, Shang X . SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data. Bioinformatics, 2022, 38( 9): 2536–2543
|
[5] |
Hänzelmann S, Castelo R, Guinney J . GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 2013, 14: 7
|
[6] |
Barbie D A, Tamayo P, Boehm J S, Kim S Y, Moody S E, .
|
[7] |
Lee E, Chuang H Y, Kim J W, Ideker T, Lee D . Inferring pathway activity toward precise disease classification. PLoS Computational Biology, 2008, 4( 11): e1000217
|
[8] |
Tomfohr J, Lu J, Kepler T B . Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics, 2005, 6: 225
|
[9] |
Mao W, Zaslavsky E, Hartmann B M, Sealfon S C, Chikina M . Pathway-level information extractor (PLIER) for gene expression data. Nature Methods, 2019, 16( 7): 607–610
|
[10] |
Su K, Yu Q, Shen R, Sun S Y, Moreno C S, Li X, Qin Z S . Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis. Cell Reports Methods, 2021, 1( 4): 100050
|
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〈 |
|
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